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Leino LI, Vesterinen EJ, Sánchez-Virosta P, Puigbò P, Eeva T, Rainio MJ. Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124434. [PMID: 38936789 DOI: 10.1016/j.envpol.2024.124434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.
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Affiliation(s)
- Lyydia I Leino
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Eero J Vesterinen
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Pablo Sánchez-Virosta
- Department of Biology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - Pere Puigbò
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland; Eurecat, Technology Centre of Catalonia, Reus, Catalonia, Spain; Department of Biochemistry and Biotechnology, Rovira I Virgili University, Tarragona, Catalonia, Spain.
| | - Tapio Eeva
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Miia J Rainio
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
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2
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Ruuskanen S. Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes. J Exp Biol 2024; 227:jeb246024. [PMID: 38449325 DOI: 10.1242/jeb.246024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.
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Affiliation(s)
- Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9C, 40500 Jyväskylä, Finland
- Department of Biology, University of Turku, Vesilinnankatu 5, 20500 Turku, Finland
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3
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Schmiedová L, Černá K, Li T, Těšický M, Kreisinger J, Vinkler M. Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time. Int Microbiol 2024; 27:127-142. [PMID: 37222909 PMCID: PMC10830831 DOI: 10.1007/s10123-023-00372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Kateřina Černá
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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4
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Florkowski MR, Hamer SA, Yorzinski JL. Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad096. [PMID: 37586886 DOI: 10.1093/femsec/fiad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
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Affiliation(s)
- Melanie R Florkowski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
| | - Sarah A Hamer
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Schubot Center for Avian Health, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 701 Farm to Market Service Road, College Station, TX 77840, United States
| | - Jessica L Yorzinski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
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5
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Liukkonen M, Hukkanen M, Cossin-Sevrin N, Stier A, Vesterinen E, Grond K, Ruuskanen S. No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings. Anim Microbiome 2023; 5:19. [PMID: 36949549 PMCID: PMC10031902 DOI: 10.1186/s42523-023-00241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. RESULTS Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. CONCLUSIONS We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland.
| | - Mikaela Hukkanen
- Department of Biology, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622, Lyon, France
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
- Department of Biology, University of Turku, Turku, Finland
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6
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Florkowski MR, Yorzinski JL. Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird. Anim Microbiome 2023; 5:8. [PMID: 36739424 PMCID: PMC9899379 DOI: 10.1186/s42523-023-00227-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior. RESULTS We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers. CONCLUSIONS Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.
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Affiliation(s)
- Melanie R. Florkowski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA
| | - Jessica L. Yorzinski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA ,grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
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7
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Ding X, Jin F, Xu J, Zhang S, Chen D, Hu B, Hong Y. The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle ( Pelodiscus sinensis). IMETA 2022; 1:e17. [PMID: 38868566 PMCID: PMC10989827 DOI: 10.1002/imt2.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2024]
Abstract
The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice-fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha-diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source-tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2-oxoglutarate, N-acetyl-d-mannosamine, cis-4-hydroxy-d-proline, nicotinamide, and l-alanine, which were significantly correlated with important categories of microbe-mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome-metabolome association.
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Affiliation(s)
- Xia Ding
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Feng Jin
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Jiawang Xu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Shulei Zhang
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Dongxu Chen
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Beijuan Hu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Yijiang Hong
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
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8
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Maraci Ö, Corsini M, Antonatou-Papaioannou A, Jünemann S, Sudyka J, Di Lecce I, Caspers BA, Szulkin M. Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic. Sci Rep 2022; 12:6872. [PMID: 35477720 PMCID: PMC9046431 DOI: 10.1038/s41598-022-10734-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Urbanisation is a major anthropogenic perturbation presenting novel ecological and evolutionary challenges to wild populations. Symbiotic microorganisms residing in the gastrointestinal tracts (gut) of vertebrates have mutual connections with host physiology and respond quickly to environmental alterations. However, the impact of anthropogenic changes and urbanisation on the gut microbiota remains poorly understood, especially in early development. To address this knowledge gap, we characterised the gut microbiota of juvenile great tits (Parus major) reared in artificial nestboxes and in natural cavities in an urban mosaic, employing two distinct frameworks characterising the urban space. Microbial diversity was influenced by cavity type. Alpha diversity was affected by the amount of impervious surface surrounding the breeding location, and positively correlated with tree cover density. Community composition differed between urban and rural sites: these alterations covaried with sound pollution and distance to the city centre. Overall, the microbial communities reflect and are possibly influenced by the heterogeneous environmental modifications that are typical of the urban space. Strikingly, the choice of framework and environmental variables characterising the urban space can influence the outcomes of such ecological studies. Our results open new perspectives to investigate the impact of microbial symbionts on the adaptive capacity of their hosts.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33619, Bielefeld, Germany.
| | - Michela Corsini
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Köning-Luise-Str. 1-3, 14195, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Joanna Sudyka
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Irene Di Lecce
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33619, Bielefeld, Germany
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
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Krumbeck JA, Turner DD, Diesel A, Hoffman AR, Heatley JJ. Skin microbiota of quaker parrots (Myiopsitta monachus) with normal feathering or feather loss via next-generation sequencing technology. J Exot Pet Med 2022. [DOI: 10.1053/j.jepm.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Gunasekaran M, Trabelcy B, Izhaki I, Halpern M. Direct Evidence That Sunbirds' Gut Microbiota Degrades Floral Nectar's Toxic Alkaloids. Front Microbiol 2021; 12:639808. [PMID: 33815326 PMCID: PMC8018289 DOI: 10.3389/fmicb.2021.639808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 12/01/2022] Open
Abstract
Orange-tufted sunbirds (Cinnyris osea) feed on the nectar of the tobacco tree (Nicotiana glauca) which contains toxic pyridine alkaloids characterized by high concentrations of anabasine and much lower concentrations of nicotine. We aimed at determining whether the gut microbiota of sunbirds harbors bacterial species that enable the birds to cope with these toxic alkaloids. An in vivo experiment that included 12 birds showed that inducing dysbiosis in sunbirds’ guts by the addition of sulfamethoxazole and trimethoprim, significantly reduced the birds’ ability to degrade anabasine (n = 3) compared to control birds (n = 3) with undisturbed microbiota. Sunbirds whose gut bacterial communities were altered by the antibacterial agents and who were fed with added nicotine, also showed a lower percentage of nicotine degradation (n = 3) in their excreta compared to the sunbirds with undisturbed microbiota (n = 3), though this difference was not significant. In an in vitro experiment, we studied the ability of Lactococcus lactis, Enterobacter hormaechei, Chryseobacterium gleum, Kocuria palustris, and Methylorubrum populi that were isolated from sunbirds’ excreta, to degrade anabasine and nicotine. By using gas chromatography-mass spectrometry (GC-MS) analysis, we successfully demonstrated, for the first time, the ability of these species to degrade the focal secondary metabolites. Our findings demonstrate the role of gut bacteria in detoxifying toxic secondary metabolites found in the N. glauca nectar. The degradation products may supply the birds with nitrogen which is scarce in nectar-rich diets. These findings support another role of bacteria in mediating the interactions between plants and their pollinators.
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Affiliation(s)
- Mohanraj Gunasekaran
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Beny Trabelcy
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Tivon, Israel
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11
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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12
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Góngora E, Elliott KH, Whyte L. Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia). Sci Rep 2021; 11:1200. [PMID: 33441848 PMCID: PMC7806582 DOI: 10.1038/s41598-020-80557-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.
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Affiliation(s)
- Esteban Góngora
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada.
| | - Kyle H Elliott
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
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Gunasekaran M, Lalzar M, Sharaby Y, Izhaki I, Halpern M. The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome. NPJ Biofilms Microbiomes 2020; 6:53. [PMID: 33188208 PMCID: PMC7666580 DOI: 10.1038/s41522-020-00161-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/20/2020] [Indexed: 12/24/2022] Open
Abstract
Sunbirds feed on tobacco tree nectar which contains toxic nicotine and anabasine secondary metabolites. Our aim was to understand the effect of nicotine and anabasine on the gut microbiota composition of sunbirds. Sixteen captive sunbirds were randomly assigned to two diets: artificial nectar either with (treatment) or without (control) added nicotine and anabasine. Excreta were collected at 0, 2, 4 and 7 weeks of treatment and samples were processed for bacterial culture and high-throughput amplicon sequencing of the 16S rRNA gene. The gut microbiome diversity of the treated and control birds changed differently along the seven-week experiment. While the diversity decreased in the control group along the first three samplings (0, 2 and 4 weeks), it increased in the treatment group. The microbiota composition analyses demonstrated that a diet with nicotine and anabasine, significantly changed the birds' gut microbiota composition compared to the control birds. The abundance of nicotine- and anabasine- degrading bacteria in the excreta of the treated birds, was significantly higher after four and seven weeks compared to the control group. Furthermore, analysis of culturable isolates, including Lactococcus, showed that sunbirds' gut-associated bacteria were capable of degrading nicotine and anabasine, consistent with their hypothesised role as detoxifying and nutritional symbionts.
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Affiliation(s)
- Mohanraj Gunasekaran
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Mount Carmel, Haifa, Israel
| | - Yehonatan Sharaby
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel.
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, Israel.
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Malik I, Batra T, Das S, Kumar V. Light at night affects gut microbial community and negatively impacts host physiology in diurnal animals: Evidence from captive zebra finches. Microbiol Res 2020; 241:126597. [PMID: 32979783 DOI: 10.1016/j.micres.2020.126597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/02/2020] [Accepted: 09/14/2020] [Indexed: 01/16/2023]
Abstract
The gastrointestinal tract (GIT) hosts a large number of diverse microorganisms, with mutualistic interactions with the host. Here, in two separate experiments, we investigated whether light at night (LAN) would affect GIT microbiota and, in turn, the host physiology in diurnal zebra finches (Taeniopygia guttata). Experiment I assessed the effects of no-night (LL) and dimly illuminated night (dim light at night, dLAN) on fecal microbiota diversity and host physiology of birds born and raised under 12 h photoperiod (LD; 12 h light: 12 h darkness). Under LL and dLAN, compared to LD, we found a significant increase in the body mass, subcutaneous fat deposition and hepatic accumulation of lipids. Although we found no difference in total 24 h food consumption, LL/ dLAN birds ate also at night, suggesting LAN-induced alteration in daily feeding times. Concurrently, there were marked differences in amplicon sequence and bacterial species richness between LD and LAN, with notable decline in Lactobacillus richness in birds under LL and dLAN. We attributed declined Lactobacillus population as causal (at least partially) to negative effects on the host metabolism. Therefore, in experiment II with similar protocol, birds under LL and dLAN were fed on diet with or without Lactobacillus rhamnosus GG (LGG) supplement. Clearly, LGG supplement ameliorated LL- and dLAN-induced negative effects in zebra finches. These results demonstrate adverse effects of unnatural lighting on GIT bacterial diversity and host physiology, and suggest the role of GIT microbiota in the maintenance of metabolic homeostasis in response to LAN environment in diurnal animals.
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Affiliation(s)
- Indu Malik
- Department of Zoology, University of Delhi, Delhi, 110 007, India
| | - Twinkle Batra
- Department of Zoology, University of Delhi, Delhi, 110 007, India
| | - Subhajit Das
- Department of Zoology, University of Delhi, Delhi, 110 007, India
| | - Vinod Kumar
- Department of Zoology, University of Delhi, Delhi, 110 007, India.
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15
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Shang W, Li S, Zhang L, Wu H, Jiang Y. The Composition of Gut Microbiota Community Structure of Jankowski's Bunting (Emberiza jankowskii). Curr Microbiol 2020; 77:3731-3737. [PMID: 32940730 DOI: 10.1007/s00284-020-02048-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/21/2020] [Indexed: 10/23/2022]
Abstract
Gut microbiota play a central role in the health of animals. The bacteria that individuals acquire as they age may therefore have a profound effect on their future fitness. Since most birds are capable of flight, they can be widely distributed in and adapted to various ecosystems. Moreover, birds are also challenged by the need to digest a wide range of food resources in their guts. However, little is known regarding how the microbial community structure in birds, especially wild birds, changes with host age. Here, we used high-throughput sequencing of the 16S rRNA V3-V4 region to depict the microbial composition and structure in the adults and nestlings of Jankowski's bunting (Emberiza jankowskii), an endangered species of bird, during the breeding season. The results showed that the phyla Proteobacteria (52.45%), Firmicutes (13.87%), Bacteroidetes (5.76%), Actinobacteria (4.95%), Planctomycetes (4.36%), Euryarchaeota (3.20%), Acidobacteria (2.59%), Fusobacteria (2.24%), and Chloroflexi (1.8%) dominated the gut microbial communities in Jankowski's bunting. There was no significant difference in the alpha diversity and richness among different age groups. There was also no significant difference in species richness and diversity between the nestlings and adults. However, we observed different bacterial compositions at the genus level. The genera Photobacterium and Brochothrix were detected only in the nestling groups (at days 3, 6, and 9), while Diplorickettsia was detected only in the adult group. In summary, this study can provide additional information regarding the intestinal microorganisms of wild passerine and grassland birds and provide theoretical evidence for methods to protect Jankowski's bunting.
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Affiliation(s)
- Weiping Shang
- College of Animal Science and Technology, Jilin Agricultural University, No. 2888, Xincheng Street, Changchun, People's Republic of China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University, No. 2888, Xincheng Street, Changchun, People's Republic of China
| | - Lishi Zhang
- College of Animal Science and Technology, Jilin Agricultural University, No. 2888, Xincheng Street, Changchun, People's Republic of China
| | - Hui Wu
- College of Life Science, Jilin Agricultural University, Changchun, People's Republic of China
| | - Yunlei Jiang
- College of Animal Science and Technology, Jilin Agricultural University, No. 2888, Xincheng Street, Changchun, People's Republic of China.
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Chen CY, Chen CK, Chen YY, Fang A, Shaw GTW, Hung CM, Wang D. Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests. MICROBIOME 2020; 8:129. [PMID: 32917256 PMCID: PMC7488855 DOI: 10.1186/s40168-020-00896-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments. RESULTS Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches' oral cavity/crop microbiota to their chicks' early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development. CONCLUSIONS Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission-passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature. Video Abstract.
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Affiliation(s)
- Cheng-Yu Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
- Department of Pathology, University of Southern California, Los Angeles, CA 90033 USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, 402204 Taiwan
| | - Yi-Ying Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Andrew Fang
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, 970301 Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115201 Taiwan
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van Veelen HPJ, Falcão Salles J, Matson KD, van der Velde M, Tieleman BI. Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata. Anim Microbiome 2020; 2:21. [PMID: 33499970 PMCID: PMC7807698 DOI: 10.1186/s42523-020-00039-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in terrestrial vertebrates. Using a novel experimental approach centered on the manipulation of the microbial environment of zebra finches Taeniopygia guttata, we carried out a study to investigate effects of the host’s microbial environment on: 1) constitutive immune function, 2) the resilience of the host cloacal microbiota; and 3) the degree to which immune function and host microbiota covary in microbial environments that differ in diversity. Results We explored immune indices (hemagglutination, hemolysis, IgY levels and haptoglobin concentration) and host-associated microbiota (diversity and composition) in birds exposed to two experimental microbial environments differing in microbial diversity. According to our expectations, exposure to experimental microbial environments led to differences related to specific antibodies: IgY levels were elevated in the high diversity treatment, whereas we found no effects for the other immune indices. Furthermore, according to predictions, we found significantly increased richness of dominant OTUs for cloacal microbiota of birds of the high diversity compared with the low diversity group. In addition, cloacal microbiota of individual females approached their baseline state sooner in the low diversity environment than females in the high diversity environment. This result supported a direct phenotypically plastic response of host microbiota, and suggests that its resilience depends on environmental microbial diversity. Finally, immune indices and cloacal microbiota composition tend to covary within treatment groups, while at the same time, individuals exhibited consistent differences of immune indices and microbiota characteristics. Conclusion We show that microbes in the surroundings of terrestrial vertebrates can influence immune function and host-associated microbiota dynamics over relatively short time scales. We suggest that covariation between immune indices and cloacal microbiota, in addition to large and consistent differences among individuals, provides potential for evolutionary adaptation. Ultimately, our study highlights that linking environmental and host microbiotas may help unravelling immunological variation within and potentially among species, and together these efforts will advance the integration of microbial ecology and ecological immunology.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands. .,Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 9811 MA, Leeuwarden, The Netherlands.
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Kevin D Matson
- Resource Ecology Group, Department of Environmental Sciences, Wageningen University, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
| | - Marco van der Velde
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
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18
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Bloomfield S, Wilkinson D, Rogers L, Biggs P, French N, Mohan V, Savoian M, Venter P, Midwinter A. Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand. Int J Syst Evol Microbiol 2020; 70:3775-3784. [PMID: 32501787 PMCID: PMC7395618 DOI: 10.1099/ijsem.0.004231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 05/05/2020] [Indexed: 11/18/2022] Open
Abstract
Six isolates of Campylobacter with similar non-standard colonial morphologies were identified during studies isolating Campylobacter from bird faeces and rivers in New Zealand. Genomic (16S rRNA gene sequencing and whole genome analysis) and phenotypic (MALDI-TOF analysis and conventional biochemical tests) showed that the isolates form a monophyletic clade with genetic relationships to Campylobacter coli/Campylobacter jejuni and Campylobacter peloridis/Campylobacter amoricus. They may be distinguished from other Campylobacter by their MALDI-TOF spectral pattern, their florid α-haemolysis, their ability to grow anaerobically at 37 °C, and on 2 % NaCl nutrient agar, and their lack of hippuricase. This study shows that these isolates represent a novel species within the genus Campylobacter for which the name Campylobacter novaezeelandiae sp. nov. is proposed. The presence of C. novaezeelandiae in water may be a confounder for freshwater microbial risk assessment as they may not be pathogenic for humans. The type strain is B423bT (=NZRM 4741T=ATCC TSD-167T).
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Affiliation(s)
- Samuel Bloomfield
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Present address: Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - David Wilkinson
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Lynn Rogers
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick Biggs
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nigel French
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Present address: New Zealand Food Safety and Science Research Centre, Massey University, Palmerston North, New Zealand
| | - Vathsala Mohan
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Present address: Livestock Improvement Corporation, Hamilton, New Zealand
| | - Matthew Savoian
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Pierre Venter
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Anne Midwinter
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Sherwin E, Bordenstein SR, Quinn JL, Dinan TG, Cryan JF. Microbiota and the social brain. Science 2019; 366:366/6465/eaar2016. [DOI: 10.1126/science.aar2016] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sociability can facilitate mutually beneficial outcomes such as division of labor, cooperative care, and increased immunity, but sociability can also promote negative outcomes, including aggression and coercion. Accumulating evidence suggests that symbiotic microorganisms, specifically the microbiota that reside within the gastrointestinal system, may influence neurodevelopment and programming of social behaviors across diverse animal species. This relationship between host and microbes hints that host-microbiota interactions may have influenced the evolution of social behaviors. Indeed, the gastrointestinal microbiota is used by certain species as a means to facilitate communication among conspecifics. Further understanding of how microbiota influence the brain in nature may be helpful for elucidating the causal mechanisms underlying sociability and for generating new therapeutic strategies for social disorders in humans, such as autism spectrum disorders (ASDs).
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Affiliation(s)
- Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN, USA
| | - John L. Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Sciences, University College Cork, Cork, Ireland
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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20
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Cockerham S, Lee B, Orben RA, Suryan RM, Torres LG, Warzybok P, Bradley R, Jahncke J, Young HS, Ouverney C, Shaffer SA. Microbial Ecology of the Western Gull (Larus occidentalis). MICROBIAL ECOLOGY 2019; 78:665-676. [PMID: 30891612 DOI: 10.1007/s00248-019-01352-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.
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Affiliation(s)
- Susan Cockerham
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA.
| | - Becky Lee
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Rachael A Orben
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
| | - Robert M Suryan
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
- Alaska Fisheries Science Center, Auke Bay Laboratories, NOAA Fisheries, 17109 Pt. Lena Loop Rd, Juneau, AK, 99801, USA
| | - Leigh G Torres
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Hatfield Marine Science Center, Newport, OR, 97365, USA
| | - Pete Warzybok
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Russell Bradley
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Jaime Jahncke
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Hillary S Young
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Cleber Ouverney
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Scott A Shaffer
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA
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21
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Diren Sigirci B, Celik B, Başaran Kahraman B, Bagcigil AF, Ak S. Tetracycline Resistance of Enterobacteriaceae Isolated From Feces of Synanthropic Birds. J Exot Pet Med 2019. [DOI: 10.1053/j.jepm.2017.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Comparative Analysis of the Gut Microbial Composition and Meat Flavor of Two Chicken Breeds in Different Rearing Patterns. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4343196. [PMID: 30410932 PMCID: PMC6206517 DOI: 10.1155/2018/4343196] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/12/2018] [Accepted: 09/04/2018] [Indexed: 01/05/2023]
Abstract
The objective of the study is to compare the effects of free-range (FR) and cage-range (CR) breeding on gut microbiota and flavor compounds of Caoke (C) and Partridge Shank chickens (Q). A total of 120 experimental chickens were assigned to FR group and CR group; each group contain both 30 Caoke chickens and 30 Partridge Shank chickens. At 154 d old, 12 chickens of each group were selected and their cecal contents were extracted and examined for the composition of gut microbiota by illumina sequencing of the V3 region of the 16S rDNA genes, and flavor compounds were analyzed through headspace-solid-phase microextraction (HS-SPME) method. The results showed that, except for acids, the amount of flavor substances in the FR group was higher than those in the CR group, especially the content of Hexanal and D-limonene. Meanwhile, the higher concentrations of carbonyls including (E,E)-2,4-decadienal, (E)-2-decenal, (E)-2-octenal, and pentanal were in the FR chicken meat, but the differences in concentrations compared with CR were not significant. High levels of ethyl hexanoate and β-ocimene were only detected in FR groups. The Firmicutes had the highest proportion of chicken cecal microbiota, whereas the Fusobacteria was only detected in the cecal samples of Q chicken in FR group. Actinobacteria was more prevalent in FR groups than in CR groups. Meanwhile, in Q chickens, the proportions of Bacteroidetes and Proteobacteria in FR group were higher than those in CR group. Using MG-RAST Subsystem Technology, we found that some genes were associated with the formation of precursors of flavor compounds or with the metabolism and degradation of aromatic compounds. Overall, CR and FR breeding influenced the gut microbiota and flavor compounds, potentially because of the changes in diet and living conditions.
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23
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Michel AJ, Ward LM, Goffredi SK, Dawson KS, Baldassarre DT, Brenner A, Gotanda KM, McCormack JE, Mullin SW, O'Neill A, Tender GS, Uy JAC, Yu K, Orphan VJ, Chaves JA. The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch. MICROBIOME 2018; 6:167. [PMID: 30231937 PMCID: PMC6146768 DOI: 10.1186/s40168-018-0555-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/05/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. RESULTS We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons. CONCLUSIONS This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.
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Affiliation(s)
- Alice J Michel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shana K Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, 90041, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Daniel T Baldassarre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Alec Brenner
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kiyoko M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, England
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, CA, 90041, USA
| | - Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ariel O'Neill
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Gabrielle S Tender
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - J Albert C Uy
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Kristie Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Quito, Ecuador.
- Galápagos Science Center, Puerto Baquerizo Moreno, Galápagos, Ecuador.
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Ruiz-Rodríguez M, Martín-Vivaldi M, Martínez-Bueno M, Soler JJ. Gut Microbiota of Great Spotted Cuckoo Nestlings is a Mixture of Those of Their Foster Magpie Siblings and of Cuckoo Adults. Genes (Basel) 2018; 9:genes9080381. [PMID: 30060541 PMCID: PMC6115760 DOI: 10.3390/genes9080381] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023] Open
Abstract
Diet and host genetic or evolutionary history are considered the two main factors determining gut microbiota of animals, although studies are scarce in natural populations. The system of great spotted cuckoos (Clamator glandarius) parasitizing magpies (Pica pica) is ideal to study both effects since magpie adults feed cuckoo and magpie nestlings with the same diet and, consequently, differences in gut microbiota of nestlings of these two species will mainly reflect the importance of genetic components. Moreover, the diet of adults and of nestling cuckoos drastically differ from each other and, thus, differences and similarities in their microbiotas would respectively reflect the effect of environmental and genetic factors. We used next-generation sequencing technologies to analyze the gut microbiota of cuckoo adults and nestlings and of magpie nestlings. The highest α-diversity estimates appeared in nestling cuckoos and the lowest in nestling magpies. Moreover, despite the greatest differences in the microbiome composition of magpies and cuckoos of both ages, cuckoo nestlings harbored a mixture of the Operational Taxonomic Units (OTUs) present in adult cuckoos and nestling magpies. We identified the bacterial taxa responsible for such results. These results suggest important phylogenetic components determining gut microbiome of nestlings, and that diet might be responsible for similarities between gut microbiome of cuckoo and magpie nestlings that allow cuckoos to digest food provided by magpie adults.
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Affiliation(s)
- Magdalena Ruiz-Rodríguez
- Biologie Integrative des Organismes Marins, Observatoire Océanologique, Sorbonne Universités, Avenue du Fontaulé, 66650 Banyuls-Sur-Mer, France.
| | - Manuel Martín-Vivaldi
- Departamento de Zoología, Universidad de Granada, E-18071 Granada, Spain.
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
| | - Manuel Martínez-Bueno
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Departamento de Microbiología, Universidad de Granada, E-18071 Granada, Spain.
| | - Juan José Soler
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (EEZA-CSIC), Ctra. Sacramento s/n, La Cañada de San Urbano, E-04120 Almería, Spain.
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25
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Carter DL, Docherty KM, Gill SA, Baker K, Teachout J, Vonhof MJ. Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1234-1241. [PMID: 30857088 DOI: 10.1016/j.scitotenv.2018.01.343] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 05/20/2023]
Abstract
The widespread use of antibiotics in human and veterinary medicine to treat pathogenic bacteria has resulted in the rapid emergence of antibiotic-resistant bacteria (ARB). Wild animals may enable the spread of pathogenic and non-pathogenic ARB when they are exposed to reservoirs (e.g., contaminated soil, water, or crops) and carry ARB in and on their bodies to other environments. We tested for the presence of ARB in four songbird species in southwest Michigan across a gradient of land use. Our specific objectives were to: 1) quantify the prevalence of ARB found in the gut microbiome of birds; 2) identify the specific bacteria exhibiting resistance; 3) assess whether ARB prevalence and identity varied among bird species; and 4) assess whether anthropogenic land use influenced the prevalence and identity of ARB found on birds. We sampled birds across a land use gradient consisting of urban, agricultural, and natural land covers using a randomized, spatially-balanced sampling design and cultured bacteria from fecal samples in the presence of three different antibiotics (amoxicillin, tetracycline, and ciprofloxacin). Overall prevalence of ARB was high, with 88% of total birds carrying ARB resistant to one of three antibiotics that we tested. Resistance to amoxicillin was more common (83% of sampled birds) than resistance to tetracycline (15%) or ciprofloxacin (1%). Identified ARB were diverse, and included 135 isolates representing 5 bacterial phyla and 22 genera. There was no effect of land use on ARB prevalence, with 90% of sampled birds captured in rural sites and 85% of sampled birds in urban sites carrying ARB. We provide the first analysis of ARB prevalence across multiple bird species and land uses utilizing a spatially-balanced, randomized study design. Our results demonstrate that nearly all sampled birds carried at least some ARB, and that they may serve as important dispersal agents of ARB across large spatial scales.
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Affiliation(s)
- Diana L Carter
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Sharon A Gill
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathleen Baker
- Department of Geography, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Jordan Teachout
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States; Institute of the Environment and Sustainability, Western Michigan University, Kalamazoo, MI 49008, United States.
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26
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van Veelen HPJ, Salles JF, Tieleman BI. Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. ISME JOURNAL 2018; 12:1375-1388. [PMID: 29445132 DOI: 10.1038/s41396-018-0067-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/01/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisation of egg microbiome assembly. Here, we investigated maternal and environmental contributions to avian eggshell microbiota in wild passerine birds: woodlark Lullula arborea and skylark Alauda arvensis. Using 16S rRNA gene sequencing, we demonstrated in both lark species, at the population and within-nest levels, that bacterial communities of freshly laid eggs were distinct from the female cloacal microbiome. Instead, soil-borne bacteria appeared to thrive on freshly laid eggs, and eggshell microbiota composition strongly resembled maternal skin, body feather and nest material communities, sources in direct contact with laid eggs. Finally, phylogenetic structure analysis and microbial source tracking underscored species sorting from directly contacting sources rather than in vivo-transferred symbionts. The female-egg-nest system allowed an integrative assessment of avian egg microbiome assembly, revealing mixed modes of symbiont acquisition not previously documented for vertebrate eggs. Our findings illuminated egg microbiome origins, which suggested a limited potential of eggshells for transgenerational transmission, encouraging further investigation of eggshell microbiome functions in vertebrates.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
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27
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Risely A, Waite D, Ujvari B, Klaassen M, Hoye B. Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions. Mol Ecol 2017; 26:5842-5854. [PMID: 28815767 DOI: 10.1111/mec.14326] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/05/2017] [Indexed: 12/21/2022]
Abstract
Migratory animals encounter suites of novel microbes as they move between disparate sites during their migrations, and are frequently implicated in the global spread of pathogens. Although wild animals have been shown to source a proportion of their gut microbiota from their environment, the susceptibility of migrants to enteric infections may be dependent upon the capacity of their gut microbiota to resist incorporating encountered microbes. To evaluate migrants' susceptibility to microbial invasion, we determined the extent of microbial sourcing from the foraging environment and examined how this influenced gut microbiota dynamics over time and space in a migratory shorebird, the Red-necked stint Calidris ruficollis. Contrary to previous studies on wild, nonmigratory hosts, we found that stint on their nonbreeding grounds obtained very little of their microbiota from their environment, with most individuals sourcing only 0.1% of gut microbes from foraging sediment. This microbial resistance was reflected at the population level by only weak compositional differences between stint flocks occupying ecologically distinct sites, and by our finding that stint that had recently migrated 10,000 km did not differ in diversity or taxonomy from those that had inhabited the same site for a full year. However, recent migrants had much greater abundances of the genus Corynebacterium, suggesting a potential microbial response to either migration or exposure to a novel environment. We conclude that the gut microbiota of stint is largely resistant to invasion from ingested microbes and that this may have implications for their susceptibility to enteric infections during migration.
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Affiliation(s)
- Alice Risely
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - David Waite
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Beata Ujvari
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia
| | - Bethany Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia.,School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
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28
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ESTABLISHING NORMAL FECAL FLORA IN WILD AUSTRALIAN PASSERINE BIRDS BY USE OF THE FECAL GRAM STAIN. J Zoo Wildl Med 2017; 48:786-793. [DOI: 10.1638/2016-0120.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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29
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Great cormorants (Phalacrocorax carbo) as potential vectors for the dispersal of Vibrio cholerae. Sci Rep 2017; 7:7973. [PMID: 28801549 PMCID: PMC5554209 DOI: 10.1038/s41598-017-08434-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/12/2017] [Indexed: 11/26/2022] Open
Abstract
Vibrio cholerae is the cause of cholera, a devastating epidemic and pandemic disease. Despite its importance, the way of its global dissemination is unknown. V. cholerae is abundant in aquatic habitats and is known to be borne by copepods, chironomids and fishes. Our aim was to determine if fish-eating birds act as vectors in the spread of V. cholerae by consuming infected fish. We determined the existence of V. cholerae in the microbiome of 5/7 wild cormorants’ intestine. In three of these V. cholerae-positive wild cormorants, the presence of a gene for cholera toxin (ctxA) was detected. We subsequently tested eight captive, hand-reared cormorants, divided into two equal groups. Prior to the experiment, the feces of the cormorants were V. cholerae-negative. One group was fed exclusively on tilapias, which are naturally infected with V. cholerae, and the other was fed exclusively on goldfish or on koi that were V. cholerae-negative. We detected V. cholerae in the feces of the tilapia-fed, but not in the goldfish/koi-fed, cormorants. Hence, we demonstrate that fish-eating birds can be infected with V. cholerae from their fish prey. The large-scale movements of many fish-eating birds provide a potential mechanism for the global distribution of V. cholerae.
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30
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Kreisinger J, Kropáčková L, Petrželková A, Adámková M, Tomášek O, Martin JF, Michálková R, Albrecht T. Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird. Front Microbiol 2017; 8:50. [PMID: 28220109 PMCID: PMC5292904 DOI: 10.3389/fmicb.2017.00050] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/06/2017] [Indexed: 12/20/2022] Open
Abstract
Animal bodies are inhabited by a taxonomically and functionally diverse community of symbiotic and commensal microorganisms. From an ecological and evolutionary perspective, inter-individual variation in host-associated microbiota contributes to physiological and immune system variation. As such, host-associated microbiota may be considered an integral part of the host’s phenotype, serving as a substrate for natural selection. This assumes that host-associated microbiota exhibits high temporal stability, however, and that its composition is shaped by trans-generational transfer or heritable host-associated microbiota modulators encoded by the host genome. Although this concept is widely accepted, its crucial assumptions have rarely been tested in wild vertebrate populations. We performed 16S rRNA metabarcoding on an extensive set of fecal microbiota (FM) samples from an insectivorous, long-distance migratory bird, the barn swallow (Hirundo rustica). Our data revealed clear differences in FM among juveniles and adults as regards taxonomic and functional composition, diversity and co-occurrence network complexity. Multiple FM samples from the same juvenile or adult collected within single breeding seasons exhibited higher similarity than expected by chance, as did adult FM samples over two consecutive years. Despite low effect sizes for FM stability over time at the community level, we identified an adult FM subset with relative abundances exhibiting significant temporal consistency, possibly inducing long-term effects on the host phenotype. Our data also indicate a slight maternal (but not paternal) effect on FM composition in social offspring, though this is unlikely to persist into adulthood. We discuss our findings in the context of both evolution and ecology of microbiota vs. host interactions and barn swallow biology.
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Affiliation(s)
- Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University Prague, Czechia
| | - Lucie Kropáčková
- Department of Zoology, Faculty of Science, Charles University Prague, Czechia
| | - Adéla Petrželková
- Department of Ecology, Faculty of Science, Charles University Prague, Czechia
| | - Marie Adámková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Studenec Czechia
| | - Oldřich Tomášek
- Department of Zoology, Faculty of Science, Charles UniversityPrague, Czechia; Institute of Vertebrate Biology, Czech Academy of Sciences, StudenecCzechia
| | - Jean-François Martin
- Montpellier-SupAgro, UMR Centre de Biologie pour la Gestion des Populations Montferrier-sur-Lez, France
| | - Romana Michálková
- Department of Zoology, Faculty of Science, Charles University Prague, Czechia
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles UniversityPrague, Czechia; Institute of Vertebrate Biology, Czech Academy of Sciences, StudenecCzechia
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31
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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32
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Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species. Symbiosis 2016. [DOI: 10.1007/s13199-016-0419-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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33
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Davies YM, Cunha MPV, Oliveira MGX, Oliveira MCV, Philadelpho N, Romero D, Milanelo L, Guimarães MB, Ferreira AJP, Moreno AM, Sá LRM, Knöbl T. Virulence and antimicrobial resistance ofKlebsiella pneumoniaeisolated from passerine and psittacine birds. Avian Pathol 2016; 45:194-201. [DOI: 10.1080/03079457.2016.1142066] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hird SM, Sánchez C, Carstens BC, Brumfield RT. Comparative Gut Microbiota of 59 Neotropical Bird Species. Front Microbiol 2015; 6:1403. [PMID: 26733954 PMCID: PMC4685052 DOI: 10.3389/fmicb.2015.01403] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 11/25/2015] [Indexed: 12/26/2022] Open
Abstract
The gut microbiota of vertebrates are essential to host health. Most non-model vertebrates, however, lack even a basic description of natural gut microbiota biodiversity. Here, we sampled 116 intestines from 59 Neotropical bird species and used the V6 region of the 16S rRNA molecule as a microbial fingerprint (average coverage per bird ~80,000 reads). A core microbiota of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria was identified, as well as several gut-associated genera. We tested 18 categorical variables associated with each bird for significant correlation to the gut microbiota; host taxonomic categories were most frequently significant and explained the most variation. Ecological variables (e.g., diet, foraging stratum) were also frequently significant but explained less variation. Little evidence was found for a significant influence of geographic space. Finally, we suggest that microbial sampling during field collection of organisms would propel biological understanding of evolutionary history and ecological significance of host-associated microbiota.
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Affiliation(s)
- Sarah M. Hird
- Museum of Natural Science, Louisiana State UniversityBaton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - César Sánchez
- Museum of Natural Science, Louisiana State UniversityBaton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology, Ohio State UniversityColumbus, OH, USA
| | - Robb T. Brumfield
- Museum of Natural Science, Louisiana State UniversityBaton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
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35
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Rodríguez-Ruano SM, Martín-Vivaldi M, Martín-Platero AM, López-López JP, Peralta-Sánchez JM, Ruiz-Rodríguez M, Soler JJ, Valdivia E, Martínez-Bueno M. The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird. PLoS One 2015; 10:e0139734. [PMID: 26445111 PMCID: PMC4596831 DOI: 10.1371/journal.pone.0139734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 12/16/2022] Open
Abstract
Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host.
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Affiliation(s)
| | | | | | | | | | - Magdalena Ruiz-Rodríguez
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain
| | - Juan J Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Granada, Spain
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36
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Kreisinger J, Čížková D, Kropáčková L, Albrecht T. Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing. PLoS One 2015; 10:e0137401. [PMID: 26360776 PMCID: PMC4567286 DOI: 10.1371/journal.pone.0137401] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 08/17/2015] [Indexed: 01/15/2023] Open
Abstract
Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species’ high level of sexual promiscuity.
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Affiliation(s)
- Jakub Kreisinger
- Studenec Research Facility, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
- Department of Zoology, Faculty of Science, Charles University Prague, Viničná 7, 128 44 Prague 2, Czech Republic
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, I-38010 San Michele all’Adige, TN, Italy
- * E-mail:
| | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Lucie Kropáčková
- Department of Zoology, Faculty of Science, Charles University Prague, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Tomáš Albrecht
- Studenec Research Facility, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
- Department of Zoology, Faculty of Science, Charles University Prague, Viničná 7, 128 44 Prague 2, Czech Republic
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Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol 2015; 6:673. [PMID: 26191057 PMCID: PMC4490257 DOI: 10.3389/fmicb.2015.00673] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/19/2015] [Indexed: 01/16/2023] Open
Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.
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Affiliation(s)
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of AucklandAuckland, New Zealand
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Benskin CMH, Rhodes G, Pickup RW, Mainwaring MC, Wilson K, Hartley IR. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus. Ecol Evol 2015; 5:821-35. [PMID: 25750710 PMCID: PMC4338966 DOI: 10.1002/ece3.1384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/04/2014] [Indexed: 11/24/2022] Open
Abstract
Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.
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Affiliation(s)
| | - Glenn Rhodes
- Centre for Ecology and Hydrology, Lancaster Environment Centre Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Roger W Pickup
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University Lancaster, LA1 4YQ, UK
| | - Mark C Mainwaring
- Lancaster Environment Centre, Lancaster University Lancaster, LA1 4YQ, UK
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University Lancaster, LA1 4YQ, UK
| | - Ian R Hartley
- Lancaster Environment Centre, Lancaster University Lancaster, LA1 4YQ, UK
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De Schryver P, Vadstein O. Ecological theory as a foundation to control pathogenic invasion in aquaculture. THE ISME JOURNAL 2014; 8:2360-8. [PMID: 24892581 PMCID: PMC4260705 DOI: 10.1038/ismej.2014.84] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 03/20/2014] [Accepted: 04/18/2014] [Indexed: 01/02/2023]
Abstract
Detrimental host-pathogen interactions are a normal phenomenon in aquaculture animal production, and have been counteracted by prophylactic use of antibiotics. Especially, the youngest life stages of cultivated aquatic animals are susceptible to pathogen invasion, resulting in disease and mortality. To establish a more sustainable aquatic food production, there is a need for new microbial management strategies that focus on 'join them' and not the traditional 'beat them' approaches. We argue that ecological theory could serve as a foundation for developing sustainable microbial management methods that prevent pathogenic disease in larviculture. Management of the water microbiota in aquaculture systems according to ecological selection principles has been shown to decrease opportunistic pathogen pressure and to result in an improved performance of the cultured animals. We hypothesize that manipulation of the biodiversity of the gut microbiota can increase the host's resistance against pathogenic invasion and infection. However, substantial barriers need to be overcome before active management of the intestinal microbiota can effectively be applied in larviculture.
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Affiliation(s)
- Peter De Schryver
- Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Olav Vadstein
- Department of Biotechnology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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40
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Vo ATE, Jedlicka JA. Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol Ecol Resour 2014; 14:1183-97. [PMID: 24774752 DOI: 10.1111/1755-0998.12269] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/20/2014] [Accepted: 04/24/2014] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI-based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post-adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250-bp, paired-end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian-specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.
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Affiliation(s)
- A-T E Vo
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
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Waite DW, Taylor MW. Characterizing the avian gut microbiota: membership, driving influences, and potential function. Front Microbiol 2014; 5:223. [PMID: 24904538 PMCID: PMC4032936 DOI: 10.3389/fmicb.2014.00223] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/28/2014] [Indexed: 12/18/2022] Open
Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill important roles in providing the host with nutrition and protection from pathogens. Although many studies have investigated the role of particular microbes in the guts of avian species, there has been no attempt to unify the results of previous, sequence-based studies to examine the factors that shape the avian gut microbiota as a whole. In this study, we present the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available clone-library and amplicon pyrosequencing data. We investigate community membership and structure, as well as probe the roles of some of the key biological factors that influence the gut microbiota of other vertebrates, such as host phylogeny, location within the gut, diet, and association with humans. Our results indicate that, across avian studies, the microbiota demonstrates a similar phylum-level composition to that of mammals. Host bird species is the most important factor in determining community composition, although sampling site, diet, and captivity status also contribute. These analyses provide a first integrated look at the composition of the avian microbiota, and serve as a foundation for future studies in this area.
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Affiliation(s)
- David W Waite
- Centre for Microbial Innovation, School of Biological Sciences, Faculty of Science, The University of Auckland Auckland, New Zealand
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, Faculty of Science, The University of Auckland Auckland, New Zealand
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Mirón L, Mira A, Rocha-Ramírez V, Belda-Ferre P, Cabrera-Rubio R, Folch-Mallol J, Cardénas-Vázquez R, DeLuna A, Hernández AL, Maya-Elizarrarás E, Schondube JE. Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.4303/mg/235853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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